1) SCRIPT_img_filename_change.py --> change file name to standardized format
2) SCRIPT_img_to_ROI_crop.py --> crop image based on ImageJ ROI
3) Segment cropped images using Cellpose (run COLAB Cellpose notebook)
4) [OPTIONAL] SCRIPT plot mask vs img.py --> overlay thresholded mask on original image, for verification
5) [OPTIONAL] SCRIPT mask npy to img.py --> Convert masks in .npy format in a directory into image format. Useful for loading into cellpose GUI for further mask labelling.
6) SCRIPT CTIP2 GFP Fos rpS6 cellpose_masks_quant --> Threshold Cellpose masks and calculate mask overlap